Hi,
I noticed that the valid values for fix_blength in Codeml.pm do not
include option "fix_blength 1: initial",
I agreed, I would add it myself in cvs:
bioperl-run/Bio/Tools/Run/Phylo/PAML/Codeml.pm
'fix_blength' => [0,-1,2],
change to:
'fix_blength' => [0,-1,1,2],
Jason?
Bests,
Albert.